DQ - I think that what is important is that, in addition to completing the two part FMM form, you should also write "RESIDENTE PERMANENTE" in block letters across the tops of both sections of the form. When you check in at the immigration window before leaving GDL and present your passport and your Residente Permanente card, sometimes the agent scribbles "RT" or "RP" on the top of the form when he's stamping everything, but sometimes they don't. If you do it, then you know it gets done. The smaller (bottom) section is what the airline agent takes from you when you check in. Stick away the larger top part of the FMM form in a safe place (and remember where that is!!) since you need it for your return.
Then when you return to Mexico, just be sure to hand the immigration agent your Residente Permanente card, along with the completed top part of the FMM form and your passport.
Buen viaje!